RBP and miRNA annotation: tasks list

[eboileau]

A clear and concise description of todo items.

• RBP and miRNA BED files were all prepared using ad hoc scripts, for human and mouse only, copied to the server, and permissions were handled by hand. Ideally, wrangling should be packaged or integrated into the CLI, but for RBP in particular, this is currently "intensive"... oRNAment has data for Ensembl gene release 97, for Homo sapiens (GRCh38), Caenorhabditis elegans (WBcel235), Danio rerio (GRCz11), Drosophila melanogaster (BDGP6) and Mus musculus (GRCm38). For miRNA, we somehow have to wrap TargetScan Perl scripts and prepare BED files for default predictions. Finally, all this has to be consistently integrated to the application, down to the API and frontend, where e.g. currently we make no difference between no results found from available data and unavailable data.

• Is it worth adding relative positions of modification within target/binding site? If we have a fixed motif/region length, this is relatively easy, otherwise this may not be possible. For RBP in particular, we have split motifs, calculating the relative position might be difficult.

• Add site-specific information (from props) to table as hidden columns for download e.g. by reformatting the object.

• Fix the width of columns/table for RBB and miRNA, so they are visually matching.